Summary

Number of simulated transcripts: 50028

Number of known transcripts: 35028

Number of novel transcripts: 15000

Number of reconstructed transcripts: 135280

Simulated counts distribution

Isoform classification distribution of reconstructed transcripts

Evaluation of simulation

Simulated transcript were grouped in know simulated transcripts which appear in the reference annotation GTF and novel simulated transcripts that were deleted from the annotation. The following metrics were computed:

  • Number of isoforms simulated: Total number of simulated isoforms
  • True Positive isoforms (TP): Isoforms that match junctions with a simulated transcript and its TSS and TTS is within the 50bp threshold
  • Partial True Positive isoforms (PTP): Isoforms that match junctions but the TSS and TTS are beyond the threshold
  • False Negative isoforms (FN) : Isoforms that were simulated but not detected
  • False Positive (FP): Transcript that were detected but not simulated
  • Sensitivity: TP/Number of simulated transcripts
  • Precision: TP/Detected isoforms
  • F-score: Harmonic mean of precision and sensitivity
  • False Discovery Rate: (FP+PTP)/Detected isoforms
  • Positive Detection Rate: (TP + PTP)/Number of simulated transcripts
  • False Detection Rate: FP/Detected isoforms

Performance metrics

Full results

Above min. supp. results

Plots full results

Mono- or multi-exon

Canonical Junctions

Number of exons

Transcript length

Expression level

Isoform complexity

Splice Junction Coverage

Plots above min. supp. results

Mono- or multi-exon

Number of exons

TableGrob (1 x 2) “arrange”: 2 grobs z cells name grob 1 1 (1-1,1-1) arrange gtable[layout] 2 2 (1-1,2-2) arrange gtable[layout]

Transcript length

TableGrob (1 x 2) “arrange”: 2 grobs z cells name grob 1 1 (1-1,1-1) arrange gtable[layout] 2 2 (1-1,2-2) arrange gtable[layout]

Expression level

TableGrob (1 x 2) “arrange”: 2 grobs z cells name grob 1 1 (1-1,1-1) arrange gtable[layout] 2 2 (1-1,2-2) arrange gtable[layout]

Isoform complexity

TableGrob (1 x 2) “arrange”: 2 grobs z cells name grob 1 1 (1-1,1-1) arrange gtable[layout] 2 2 (1-1,2-2) arrange gtable[layout]